"And what you fail to realize is that my ship is dragging mines."
Just before that: "It doesn't take a great actor to recognize a bad one - you're sweating!"
"By Grabthar's hammer...by the suns of Worvan...you shall be avenged." Followed shortly by Alan Rickman killing an alien with his bare hands,and kicking prodigious amounts of ass in what can only be described as a berserk fury. Think about that for a moment. He's an actor, armed with nothing more than his fists and whatever he can get his hands on, up against a horde of battle hardened alien soldiers who have directed energy weapons and body armor. When we see him later, all evidence shows that he was winning.
Fred Kwan taking down a room full of alien baddies by beaming a rock monster up from the planet's surface. Made even better by his line as he watches with unmistakable glee.
Fred: It's the simple things in life you treasure.
(meanwhile, Rocky's throwing the soldiers around like toys)
The self-destruct override apparently failing only to kick in just before the timer reaches zero. Cue a moment of bewilderment for both characters and audience before Gwen hangs the metatextual lampshade: "It always stops at one on the show." Payoff!
Brandon (the fan who accidentally got the communicator) has one fairly late in the movie. When Captain Nesmith calls him to ask some technical questions about the ship, Brandon tries to explain that he knows it's not real, that it's only a show. The Captain cuts him off to tell him it's all real, to which he responds "OH I KNEW IT!!!!" And every Star Trek fan in the audience had a CMoA of "If only...".
Don't forget Brandon and his friends' coordinated effort to guide Jason and Gwen, as well as providing visual landing markers for the incoming ship.
Mathesar beating up Sarris with a cane despite being put through brutal torture not too long ago?
Mathesar taking command of the Protector.
Mathesar: On, Teb, on!
Technically, not even part of the movie. After the credits, there's no teaser scene, just Mathesar echoing the motto of the crew of the Protector: